MzTabExporter

This application converts several OpenMS XML formats (featureXML, consensusXML, and idXML) to mzTab.

pot. predecessor tools	MzTabExporter	potential successor tools
ProteinQuantifier		external tools (MS Excel, OpenOffice, Notepad)

See the mzTab specification for details on the format.

Experimental classes:

This algorithm and underlying format is work in progress and might change.

Note

Currently mzIdentML (mzid) is not directly supported as an input/output format of this tool. Convert mzid files to/from idXML using IDFileConverter if necessary.

The command line parameters of this tool are:

MzTabExporter -- Exports various XML formats to an mzTab file.
Version: 2.0.0 May 16 2015, 09:22:21, Revision: GIT-NOTFOUND

Usage:
  MzTabExporter <options>

Options (mandatory options marked with '*'):
  -in_feature <file>    FeatureXMLs used to generate the mzTab file. (valid formats: 'featureXML')
  -in_consensus <file>  ConsensusXMLs used to generate the mzTab file. (valid formats: 'consensusXML')
  -in_id <file>         Identifications used to generate the mzTab file. (valid formats: 'idXML')
  -out <file>*          Output file (mzTab) (valid formats: 'csv')
                        
Common TOPP options:
  -ini <file>           Use the given TOPP INI file
  -threads <n>          Sets the number of threads allowed to be used by the TOPP tool (default: '1')
  -write_ini <file>     Writes the default configuration file
  --help                Shows options
  --helphelp            Shows all options (including advanced)

INI file documentation of this tool:

Legend:

required parameter

advanced parameter

+MzTabExporterExports various XML formats to an mzTab file.

version2.0.0 Version of the tool that generated this parameters file.

++1Instance '1' section for 'MzTabExporter'

in_feature FeatureXMLs used to generate the mzTab file.input file*.featureXML

in_consensus ConsensusXMLs used to generate the mzTab file.input file*.consensusXML

in_id Identifications used to generate the mzTab file.input file*.idXML

out Output file (mzTab)output file*.csv

log Name of log file (created only when specified)

debug0 Sets the debug level

threads1 Sets the number of threads allowed to be used by the TOPP tool

no_progressfalse Disables progress logging to command linetrue,false

forcefalse Overwrite tool specific checks.true,false

testfalse Enables the test mode (needed for internal use only)true,false